4D5D

Crystal structure of CymA from Klebsiella oxytoca

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

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Literature

Outer-membrane translocation of bulky small molecules by passive diffusion.

van den Berg, B., Prathyusha Bhamidimarri, S., Dahyabhai Prajapati, J., Kleinekathofer, U., Winterhalter, M.

(2015) Proc Natl Acad Sci U S A 112: E2991-E2999

  • DOI: 10.1073/pnas.1424835112
  • Primary Citation of Related Structures:  
    4D51, 4D5B, 4D5D, 4V3G, 4V3H

  • PubMed Abstract: 

    • The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels ...

    The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels. As a consequence, there is an "OM size-exclusion limit," and the uptake of bulky molecules with molecular masses of more than ∼ 600 Da is thought to be mediated by TonB-dependent, active transporters. Intriguingly, the OM protein CymA from Klebsiella oxytoca does not depend on TonB but nevertheless mediates efficient OM passage of cyclodextrins with diameters of up to ∼ 15 Å. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded β-barrel with a large pore that is occluded on the periplasmic side by the N-terminal 15 residues of the protein. Representing a previously unidentified paradigm in OM transport, CymA mediates the passive diffusion of bulky molecules via an elegant transport mechanism in which a mobile element formed by the N terminus acts as a ligand-expelled gate to preserve the permeability barrier of the OM.

    Organizational Affiliation: 

    School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYMAA, B339Klebsiella oxytocaMutation(s): 0 
Gene Names: cymA
Membrane Entity: Yes 
UniProt
Find proteins for Q48391 (Klebsiella oxytoca)
Explore Q48391 
Go to UniProtKB:  Q48391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48391
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)C, E 6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22307HL
GlyCosmos:  G22307HL
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)D, F 7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G01435GL
GlyCosmos:  G01435GL
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900015
Query on PRD_900015		C, Ealpha-cyclodextrinOligosaccharide / Drug delivery Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900012
Query on PRD_900012		D, Fbeta-cyclodextrinOligosaccharide / Drug delivery Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.16α = 90
b = 77.991β = 90
c = 109.927γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Source and taxonomy
  • Version 1.2: 2015-06-24
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Advisory, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary